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Digging through the Pokémon games years after everyone else already did because Wynaut? Here's some random finds.

Ruby/Sapphire | Diamond/Pearl

Ruby/Sapphire

Early Game Titles

First image is from field_c102.ev, and second image is from saveflag.h.
The comments show "藍バージョン" and 朱バージョン", which could be translated as Indigo Version and Crimson Version.
There are also other possible translations for 朱, such as scarlet or vermillion. It is unknown whether Game Freak actually considered using these
as the titles, if they were abbreviations for the games, or if they were tentative titles to use until the names "Sapphire" and "Ruby" were decided on.
Thanks to KmiE_821 for helping with this.

Early Evil Team Names

There are some mentions of マリン団 and トンネル団, or Team Marine and Team Tunnel in the source code.
These are likely early names for Team Aqua and Team Magma.

Pokémon Ideas

These are some ideas for Pokémon that were found in a few different lists.
Some of these Pokémon have names and sprites, while others only have a description.
A few of them may have also inspired or been reused for Pokémon in later generations.

Sprite Name Description
リィブラ
Libra		 Hummingbird Pokémon
The smallest bird Pokemon. It has many strap-like strings attached to the back of its head. It puts nectar from flowers on these straps. It flaps its wings 8,000 times per second, making it powerful and light. It can remain still in the air. Its beak is long and slender, making it ideal for sucking nectar from flowers. When it gets full, it attaches it to the back of its head. There is an “8” mark on its belly.
シャコカク
Shakokaku		 Water-cleaning Pokémon
It unleashes punches with large claws as a weapon. It has beautiful patterns on its body. It is an underwater cleaner. It looks like a mantis shrimp that evolved to be bipedal. (Replaced by Dusclops)
クジャッタ
Kujatta		 Peacock Pokémon
From the front, it looks like a peacock spreading its wings, but from the side, its wings are round with multiple layers. It looks like a semicircle. It cannot actually fly.
ニンフ
Nymph		 Mitsuuchi Pokémon
Bug Pokemon. Carpenter bee + wasp. It has three fan-like wings. No matter if there’s danger or something good, it will never let the other party know.
ジーランス
Relicanth		 A Pokémon that lives in the deep sea. Its eyes have degenerated, giving it a blank stare. It moves slowly and is rumored to be an ancient fish.
ボヤット
Boyatto		 2 stage pure Ice-type Pokémon. This is the second stage. It may have been replaced by Glalie.
Name/Concept Description
Chipmunk + Bear Pokémon It has a large tail that it uses as a pillow when it sleeps.
ドラズム
Dorazumu		 A Pokémon that beats bamboo. It looks like a snowman, but is only about 1 meter tall. It holds a large stick of bamboo in its left hand and a drumstick in its right hand. It is always happily hitting the bamboo. It is said that on some nights, many of them gather to hold a large concert.
Sea slug Pokémon Sea slug Pokémon with a beautiful tail. When it gets scared, it drops its flower-like tail and runs away while the enemy is distracted by it.
ピクス Pikusu Plastic Pokémon. It was born in a chemical plant. When plastic is thrown away in the forest or on the road, it will hunt you down with terrifying force. Be careful!
シュワッチ
Shuwacchi		 Sign Language Pokémon. It is always trying to express something with its hands and mouth. It is a gentle and quiet Pokemon. It never makes a sound.
Electric eagle Pokemon Fierce and strong-willed. A bird of prey. It has large feet and can grab a Rattata with one foot. It has frighteningly good eyesight and can spot a Rattata from 1 km away.
Diving Pokemon It is a fairly large Pokémon and can fit a person in its mouth. Submarine + football fish (anglerfish) Pokemon.
Chilly Pokémon It is said that if you are walking and find a chilly place, this Pokemon will be there. A ghost Pokemon that looks like a pale ghost woman.
It always carries delicious-looking fruits with it. But, when attacked, it drops them and runs away. The attacker is lured by the delicious-looking food it left behind and stops chasing it. Then, it escapes.
Horsetail Pokémon Its tail is a horsetail. When it runs quickly, it will come off. However, it is rumored that they breed in that location. Apparently, the horsetail part of its tail is delicious.

Other Pokémon Ideas

Dachshund, Eagle, Goat, Shark (suckerfish, evolves into large shark), Lion, Peafowl, Mosquito, Panda, Rabbit, Hippo, Skunk, Penguin, Koala, Jewel beetle, Unicorn (corn), Clione, Pig, Tanuki, Pillbug, Flounder (kappa evolution), Antlion larva, Mole, Moai, Typhoon, Parrot, Diving beetle (rear bubbles), Hanuman, Soap bubble

Rhythm (taiko), Gachinko, Egg dance, Parasitism (various Pokemon skulls), Spotted Pokemon, Piggyback Pokemon (grasshopper, hippo), Carrying Pokemon, Clock Pokemon, Pokemon with one bigger hand, Pixel Pokemon (Porygon Pre-evolution), Scarecrow, Mermaid, Snorlax pre-evolution (we will find out why it started eating and sleeping all the time)

Early Pokémon Names

Some Pokémon had different names early on. Most of these are from the file pokeyofs.h while Treecko's old name can be found in
several other files including opselect.c, message.c, message.h, ev_win.c, and r110_r0108.mes.

Pokemon Early Name Final Name (Japanese) Notes
Treecko ジュモリ (Jumori) キモリ (Kimori) from 樹 ju (trees) and 森 mori (forest)
Seedot ダングリ (Danguri) タネボー (Tanebō) どんぐり donguri (acorn)
Breloom グラッソー (Gurassō) キノガッサ (Kinogassa) possibly from grass and 草 sou (grass)?
Grumpig ツイストン (Tsuisuton) ブーピッグ (Būpiggu) from twist and 豚 ton (pig)
Plusle プラポ (Purapo) プラスル (Purasuru)
Minun マイラ (Maira) マイナン (Mainan)
Altaria アルタリス (Arutarisu) チルタリス (Chirutarisu) Closer to its final English name
Ralts エクティ (Ekuti) ラルトス (Rarutosu)
Metang アイアング (Aiangu) メタング (Metangu) from iron
Jirachi エリーム (Erīmu) ジラーチ (Jirāchi)
Deoxys ユニージェ (Yunīje) デオキシス (Deokishisu)

Additionally, Flannery used to have a different name: アイリ (Airi).

Unused in-game trades

There are 3 in-game trades that went unused in Ruby and Sapphire. Below is a table of them.

For the trades that did make it into the final game, the ability is set to either 0 or 1, which seems to correspond to one of the Pokémon's two abilities,
but for the unused trades, the numbers are higher than 1. This could mean that at the time the trades were created, abilities were set using their index numbers
instead of by a Pokémon's first/second ability. However, they are slightly off from the correct number. Walrein's ability is set to 48 (Early Bird), which is 1 off from 49 (Thick Fat)
Duskull's is set to 23 (Shadow Tag) when it normally has 26 (Levitate). As for Seedot, 5 is nowhere near the correct number for its ability, which may mean that the order of abilities
was shifted around during development.

Walrein's held item may also be an error. Just 1 slot behind Sharp Beak is the Mystic Water, which would probably be more fitting for a Walrein.

Location Requested Given Nickname IVs Contest Stats Ability ID Held Item PV OT Sheen
Rustboro City グリグリ (Guriguri) 4/4/4/4/4/4 10/10/10/10/10 5 22636 Great Ball 10000 ゲーフリ (Game Freak) (♀) 10
Dewford Town ウロウロ (Urouro) 4/4/4/4/4/4 10/10/10/10/10 26 22636 Bead Mail 20000 ゲーフリ (Game Freak) (♂) 10
Sootopolis City ブヨブヨ (Buyobuyo) 4/4/4/4/4/4 20/20/20/20/40
(High Toughness)		 48 22636 Sharp Beak 30000 ゲーフリ (Game Freak) (♀) 40

Birch's Rewards

At one point, there were 162 Pokémon in the Hoenn Pokédex instead of the 202 that are in the final game. This included all newly introduced Gen III Pokémon
except possibly Chimecho, and only 28 Pokémon returning from previous generations. In the final game, there are 67 returning Pokémon.
It is not certain if they planned to leave it at 162 Pokémon or if it was just incomplete.

Professor Birch would congratulate the player for completing the Pokédex if they had 160 or more Pokémon. (Jirachi and Deoxys are not required)
Birch would also reward the player with different items depending on their progress with the Pokédex:
10+ Pokémon : Great Ball
30+ Pokémon : Exp. Share
50+ Pokémon : Dowsing Machine

In the final game, this does not happen, and the items are found elsewhere.

The Berry Master's Neighbor


The Berry Master on Route 123 used to have a neighbor. There was an old man who would ask to see a certain Pokémon and
reward the player if it was big enough. Two NPCs with the same function exists in the final game, but they are in Sootopolis city.
Next to the Berry Master's house, there is no longer a second house, and a small lake takes its place.

Berry Mechanics - Light & Temperature


It was planned to have the environment affect the growth of berries, with factors like light exposure and temperature.
You also would have been able to plant berries in more places, including caves and houses.

There are 5 categories of temperatures. They are determined by both the type of map and the weather.
If the temperature of the environment matches the berry’s ideal temperature, the growth time will be ¼ of the normal time.
If they do not match, the growth time will be doubled (making it slower), and the light exposure check will not be performed.

Similarly to the temperature, if the berry is exposed to the right amount of light, growth time will be reduced by ¼.
The details for each individual berry can be found in ポケモン_ﾙﾋﾞｰ･ｻﾌｧｲｱ\ポケモン_ﾙﾋﾞｰ･ｻﾌｧｲｱ\タネ仕様/タネのデータ011102.xls

Temperature Location Weather
Hot Town, city, road Harsh sunlight
Cold Sea, water, ice Ash, rain, thunder, mist, snow
Normal Anything other than the above two
Hot or Normal Hot or Normal
Cold or Normal Cold or Normal

Light level Location
TOWN Town, city, road, cave, water, sea, ice, room
TCR Town, city, road
TC Town, city

Diamond/Pearl

Obtaining the Alarm Clock and Stopwatch Poketch Apps

It is already known that these two apps went unused, but not how they were meant to be obtained. It has been assumed that they were intended to be distributed
at an event, but there is a script in the game to obtain them. In Pal Park, there is a girl who will give you Poketch apps if you show her certain Pokémon.
She exists in the final game, but the player can only receive the Color Changer app and Kitchen Timer app by showing her a Kecleon or Snorlax respectively.
She has an unused script to give the player the Alarm Clock app if she is shown a Loudred, and the Stopwatch app if she is shown a Voltorb.

The text for this script remains untranslated. Below is my own translation of the text (using the translations for the others as a reference).

Alarm Clock

Japanese English
えーっとね……
あしを　ふみならして
おおごえを　だしてる　ポケモン！
 Let me see...
A Pokémon that stomps its feet
and shouts loudly!
あら！　ドゴーム！　すてき！
あたしも　ドゴームを　モチーフにした
ポケッチアプリ　もってるの！
みせてくれた　おれいに　あげるね！
 Oh! A LOUDRED! How lovely!
I have a Pokétch app that has
a LOUDRED motif.
You can have it for showing me a real LOUDRED!

Stopwatch

Japanese English
えーっとね……
モンスターボールみたいで
そうじゃない　ポケモン！
 Let me see...
A Pokémon that looks like a Poké Ball
but isn't one!
あら！　ビリリダマ！　しびれる！
あたしも　ビリリダマを　あしらった
ポケッチアプリ　もってるの！
みせてくれた　おれいに　あげるね！
 Oh! A VOLTORB! I'm tingling!
I have a Pokétch app that features
a VOLTORB design.
You can have it for showing me a real VOLTORB!

Sudowoodo Sound


From 2006/06/23 build
The very last sound effect is called SE-USSOKI (Sudowoodo's Japanese name). As expected, it plays a sound of Sudowoodo shaking, similar to the one
that appears in GSC and RSE. However, there is no Sudowoodo event in Diamond/Pearl. It can only be found in the tall grass.
It is unknown where it would have appeared in the overworld if at all, but one theory is that it may have been on Route 210 in place of the Psyduck.
Bonsly can also be found on that route.

Diamond/Pearl Battle Factory

There are many mentions of a Battle Factory in Diamond/Pearl's source code, but the Battle Factory would not appear until Platinum.
Other than the Battle Tower, it is the only battle facility of the Battle Frontier that appears here.

There is also a BGM track called BF-FACT, which likely stands for Battle Frontier Factory, but it is the same as the Gym theme.